Hyper-V Deleted Snapshot Issue

We accidentally deleted a hyper-v snapshot from the windows explorer view without merging it back into the main .vhd file and since it was such a big file it skipped the recycle bin. Now before removing this snapshot file in windows explorer we had in the past removed the snapshot via the GUI. We just never knew we needed to merge the files back into the main .vhd. The reason we removed the snapshot .avhd file was because we needed to expand our virtual hard drive size and it said we couldn't as snapshots existed. Hence we figured since we had removed the snapshot via the GUI that the file could be removed safely. We found out wrong.

When we went and booted up the original .vhd it set us back four months in time and we had to restore our windows server from backups to bring it up to date. Now our virtual machine is currently running and we can power it off and back on with loosing any data but we have noticed a difference in the vm's behavior since the night we recovered. Other virtual machines that are running will update the time stamp on the .vhd file as time goes on. This .vhd that we reverted back to and then restored on top of does not update the .vhd file time stamp. The only time that .vhd file time stamp gets updated is when the virtual machine is powered off and back on.

I understand that when the snapshot was removed without being remerged it got rid of a portion of time. How can we get our .vhd file to go back to updating properly? Any suggestions? This is a production server so we need to get this fixed so any help is really appreciated.